High resolution spectroscopy has opened the way for new, detailed study of exoplanet atmospheres. There is evidence that this technique can be sensitive to the complex, three-dimensional (3D) atmospheric structure of these planets. In this work, we perform cross correlation analysis on high resolution (R~100,000) CRIRES/VLT emission spectra of the Hot Jupiter HD 209458b. We generate template emission spectra from a 3D atmospheric circulation model of the planet, accounting for temperature structure and atmospheric motions---winds and planetary rotation---missed by spectra calculated from one-dimensional models. In this first-of-its-kind analysis, we find that using template spectra generated from a 3D model produces a more significant detection (6.9 sigma) of the planets signal than any of the hundreds of one-dimensional models we tested (maximum of 5.1 sigma). We recover the planets thermal emission, its orbital motion, and the presence of CO in its atmosphere at high significance. Additionally, we analyzed the relative influences of 3D temperature and chemical structures in this improved detection, including the contributions from CO and H2O, as well as the role of atmospheric Doppler signatures from winds and rotation. This work shows that the Hot Jupiters 3D atmospheric structure has a first-order influence on its emission spectra at high resolution and motivates the use of multi-dimensional atmospheric models in high-resolution spectral analysis.
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